How to use cummeRbund to draw plots after processing cuffdiff? (cuffdiff does not output .sqlite file as it should)

Question: (Closed) How to use cummeRbund to draw plots after processing cuffdiff? (cuffdiff does not output .sqlite file as it should)

13 months ago by

yusheng_tan • 0

yusheng_tan • 0 wrote:

Hello,

I created a workflow having Cuffdiff in the end, which outputs the last file, .sqlite file, to serve the CummeRbund. However, it does not work. No .sqlite file was output. Even though after that I added the module of CummeRbund in the workflow, connected with Cuffdiff, it just does not work. Still, no .sqlite file was output and no result for cummeRbund.

So I wonder the method to output .sqlite file though Cuffdiff and then plot the DEGs results in CummeRbund and how it could work like in a workflow.

Thank you so much.

Have a good day, Yusheng

rna-seq galaxy cufflinks • 859 views

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modified 13 months ago by Jennifer Hillman Jackson ♦ 25k • written 13 months ago by yusheng_tan • 0

Hello yusheng_tan!

Questions similar to yours can already be found at:

Cuffdiff 2.2.1.5 error with cummeRbund SQlite. "Fatal error: Exit code 1 () -- use version 2.2.1.3 instead

We have closed your question to allow us to keep similar content in the same thread.

If you disagree with this please tell us why in a reply below. We'll be happy to talk about it.

Cheers!

ADD REPLY • link written 3 months ago by Jennifer Hillman Jackson ♦ 25k

13 months ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

What version of Galaxy is your server and what version of Cuffdiff did you install?

An earlier version of Cuffdiff 2.2.1.3 is installed at https://usegalaxy.org (and the SQlite function works).

We will upgrading/testing to the 2.2.1.5 version (the most current version in the Tool Shed). As far as I know, there are no issues with it reported so far with respect to this function.

But, please follow here for updates and testing of the latest version in the latest version of Galaxy (a pre-release version of 17.09): https://github.com/galaxyproject/usegalaxy-playbook/issues/50

For now, double check the install and consider using the earlier version if you need to do this work right now. Or, wait and follow the testing of the newer version and then use once is confirmed to be successful.

Thanks for reporting the problem, Jen, Galaxy team

ADD COMMENT • link written 13 months ago by Jennifer Hillman Jackson ♦ 25k

Update: The SQLite option has been confirmed to be problematic with Cuffdiff 2.2.1.5 at https://usegalaxy.org. Please follow the same ticket above for updates.

Meanwhile, Cuffdiff 2.2.1.3 can be used. If the failed 2.2.1.5 job's tool form is brought up using the rerun button, you can switch using the Versions menu at the top of the form and the original data will populate into that tool form. Or, you can just start over using the tool directly from the tool panel.

If you are working at your own server, install the 2.2.1.3 version.

ADD REPLY • link modified 8 months ago • written 8 months ago by Jennifer Hillman Jackson ♦ 25k

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